Extending the coverage of spectral libraries: A neighbor-based approach to predicting intensities of peptide fragmentation spectra

SQID: An Intensity-Incorporated Protein Identification Algorithm for Tandem Mass Spectrometry

(2011) Wenzhou Li et al.   JOURNAL OF PROTEOME RESEARCH

Large Improvements in MS/MS-Based Peptide Identification Rates using a Hybrid Analysis

(2011) William R. Cannon et al.   JOURNAL OF PROTEOME RESEARCH

Spectrum-to-Spectrum Searching Using a Proteome-wide Spectral Library

(2011) Chia-Yu Yen et al.   MOLECULAR & CELLULAR PROTEOMICS

A semi-empirical approach for predicting unobserved peptide MS/MS spectra from spectral libraries

(2011) Yingwei Hu et al.   PROTEOMICS

Understanding the improved sensitivity of spectral library searching over sequence database searching in proteomics data analysis

(2011) Xin Zhang et al.   PROTEOMICS

On the Accuracy and Limits of Peptide Fragmentation Spectrum Prediction

(2010) Sujun Li et al.   ANALYTICAL CHEMISTRY

The Importance of Peptide Detectability for Protein Identification, Quantification, and Experiment Design in MS/MS Proteomics

(2010) Yong Fuga Li et al.   JOURNAL OF PROTEOME RESEARCH

Artificial Decoy Spectral Libraries for False Discovery Rate Estimation in Spectral Library Searching in Proteomics

(2009) Henry Lam et al.   JOURNAL OF PROTEOME RESEARCH

How does multiple testing correction work?

(2009) William S Noble   NATURE BIOTECHNOLOGY

A simple workflow to increase MS2 identification rate by subsequent spectral library search

(2009) Erik Ahrné et al.   PROTEOMICS

Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification

(2008) A. A. Klammer et al.   BIOINFORMATICS

Building consensus spectral libraries for peptide identification in proteomics

(2008) Henry Lam et al.   NATURE METHODS